src/integrators/VelocityVerletIntegrator.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file VelocityVerletIntegrator.cpp
 * @author tlin
 * @date 11/09/2004
 * @time 16:16am
 * @version 1.0
 */

#include "integrators/VelocityVerletIntegrator.hpp"
#include "integrators/DLM.hpp"

namespace oopse {
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { 
    dt2 = 0.5 * dt;
    rotAlgo = new DLM();
    rattle = new Rattle(info);
}

VelocityVerletIntegrator::~VelocityVerletIntegrator() { 
    delete rotAlgo;
    delete rattle;
}

void VelocityVerletIntegrator::initialize(){

    forceMan_->init();

    // remove center of mass drift velocity (in case we passed in a configuration
    // that was drifting
    velocitizer_->removeComDrift();

    // initialize the forces before the first step
    calcForce(true, true);

    //execute constraint algorithm to make sure at the very beginning the system is constrained  
    if (info_->getNGlobalConstraints() > 0) {
        rattle->constraintA();
        calcForce(true, true);
        rattle->constraintB();        
        info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
    }

    if (needVelocityScaling) {
        velocitizer_->velocitize(targetScalingTemp);
    }
    
    dumpWriter = createDumpWriter();
    statWriter = createStatWriter();

    dumpWriter->writeDump();

    //save statistics, before writeStat,  we must save statistics
    thermo.saveStat();
    saveConservedQuantity();
    statWriter->writeStat(currentSnapshot_->statData);

    currSample = sampleTime + currentSnapshot_->getTime();
    currStatus =  statusTime + currentSnapshot_->getTime();;
    currThermal = thermalTime +  + currentSnapshot_->getTime();
    needPotential = false;
    needStress = false;       
   
}
        
void VelocityVerletIntegrator::doIntegrate() {


    initialize();

    while (currentSnapshot_->getTime() < runTime) {
        
        preStep();

        integrateStep();
        
        postStep();

    }

    finalize();
    
}


void VelocityVerletIntegrator::preStep() {
        double difference = currentSnapshot_->getTime() + dt - currStatus;

        if (difference > 0 || fabs(difference) < oopse::epsilon) {
            needPotential = true;
            needStress = true;   
        }

}

void VelocityVerletIntegrator::postStep() {

        //save snapshot
        info_->getSnapshotManager()->advance();

        //increase time
        currentSnapshot_->increaseTime(dt);        
        
        if (needVelocityScaling) {
            if (currentSnapshot_->getTime() >= currThermal) {
                velocitizer_->velocitize(targetScalingTemp);
                currThermal += thermalTime;
            }
        }

        if (currentSnapshot_->getTime() >= currSample) {
            dumpWriter->writeDump();
            currSample += sampleTime;
        }

        if (currentSnapshot_->getTime() >= currStatus) {
            //save statistics, before writeStat,  we must save statistics
            thermo.saveStat();
            saveConservedQuantity();
            statWriter->writeStat(currentSnapshot_->statData);

            needPotential = false;
            needStress = false;
            currStatus += statusTime;
        }

        
}


void VelocityVerletIntegrator::finalize() {

    dumpWriter->writeDump();

    delete dumpWriter;
    delete statWriter;

    dumpWriter = NULL;
    statWriter = NULL;
    
}

void VelocityVerletIntegrator::integrateStep() { 

    moveA();
    calcForce(needPotential, needStress);
    moveB();
}


void VelocityVerletIntegrator::calcForce(bool needPotential,
                                         bool needStress) { 
    forceMan_->calcForces(needPotential, needStress);
}

DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
    return new DumpWriter(info_, info_->getDumpFileName());
}

StatWriter* VelocityVerletIntegrator::createStatWriter() {
    return new StatWriter(info_->getStatFileName());
}


} //end namespace oopse
Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (21 years, 4 months ago) by tim
File size:	6057 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	1722	*
4	tim	1927	* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40	tim	1722	*/
41	tim	1927
42	tim	1725	/**
43			* @file VelocityVerletIntegrator.cpp
44			* @author tlin
45			* @date 11/09/2004
46			* @time 16:16am
47			* @version 1.0
48			*/
49
50	tim	1722	#include "integrators/VelocityVerletIntegrator.hpp"
51	tim	1820	#include "integrators/DLM.hpp"
52	tim	1722
53			namespace oopse {
54	tim	1820	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
55	tim	1901	dt2 = 0.5 * dt;
56	tim	1820	rotAlgo = new DLM();
57	tim	1901	rattle = new Rattle(info);
58	tim	1819	}
59	tim	1722
60	tim	1820	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
61			delete rotAlgo;
62	tim	1901	delete rattle;
63	tim	1820	}
64	tim	1722
65	tim	1819	void VelocityVerletIntegrator::initialize(){
66	tim	1722
67	tim	1912	forceMan_->init();
68
69	tim	1725	// remove center of mass drift velocity (in case we passed in a configuration
70			// that was drifting
71	tim	1819	velocitizer_->removeComDrift();
72	tim	1722
73	tim	1725	// initialize the forces before the first step
74	tim	1819	calcForce(true, true);
75	tim	1722
76	tim	1725	//execute constraint algorithm to make sure at the very beginning the system is constrained
77	tim	1907	if (info_->getNGlobalConstraints() > 0) {
78			rattle->constraintA();
79			calcForce(true, true);
80	tim	1910	rattle->constraintB();
81			info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
82	tim	1907	}
83	tim	1725
84	tim	1819	if (needVelocityScaling) {
85			velocitizer_->velocitize(targetScalingTemp);
86	tim	1725	}
87	tim	1819
88			dumpWriter = createDumpWriter();
89			statWriter = createStatWriter();
90	tim	1725
91	tim	1820	dumpWriter->writeDump();
92	tim	1847
93	tim	1868	//save statistics, before writeStat, we must save statistics
94	tim	1847	thermo.saveStat();
95			saveConservedQuantity();
96	tim	1868	statWriter->writeStat(currentSnapshot_->statData);
97	tim	1847
98	tim	1868	currSample = sampleTime + currentSnapshot_->getTime();
99			currStatus = statusTime + currentSnapshot_->getTime();;
100			currThermal = thermalTime + + currentSnapshot_->getTime();
101			needPotential = false;
102			needStress = false;
103	tim	1820
104	tim	1819	}
105
106			void VelocityVerletIntegrator::doIntegrate() {
107	tim	1725
108
109	tim	1819	initialize();
110	tim	1725
111	tim	1819	while (currentSnapshot_->getTime() < runTime) {
112
113			preStep();
114	tim	1725
115	tim	1819	integrateStep();
116
117			postStep();
118
119			}
120
121			finalize();
122
123			}
124
125
126			void VelocityVerletIntegrator::preStep() {
127			double difference = currentSnapshot_->getTime() + dt - currStatus;
128
129			if (difference > 0 \|\| fabs(difference) < oopse::epsilon) {
130			needPotential = true;
131			needStress = true;
132	tim	1725	}
133
134	tim	1819	}
135
136			void VelocityVerletIntegrator::postStep() {
137	tim	1820
138			//save snapshot
139			info_->getSnapshotManager()->advance();
140
141			//increase time
142			currentSnapshot_->increaseTime(dt);
143	tim	1756
144	tim	1819	if (needVelocityScaling) {
145			if (currentSnapshot_->getTime() >= currThermal) {
146			velocitizer_->velocitize(targetScalingTemp);
147	tim	1725	currThermal += thermalTime;
148			}
149			}
150
151	tim	1819	if (currentSnapshot_->getTime() >= currSample) {
152	tim	1820	dumpWriter->writeDump();
153	tim	1725	currSample += sampleTime;
154			}
155
156	tim	1819	if (currentSnapshot_->getTime() >= currStatus) {
157	tim	1868	//save statistics, before writeStat, we must save statistics
158			thermo.saveStat();
159			saveConservedQuantity();
160	tim	1820	statWriter->writeStat(currentSnapshot_->statData);
161	tim	1868
162	tim	1819	needPotential = false;
163			needStress = false;
164	tim	1725	currStatus += statusTime;
165			}
166	tim	1820
167
168	tim	1819	}
169	tim	1725
170
171	tim	1819	void VelocityVerletIntegrator::finalize() {
172	tim	1725
173	tim	1820	dumpWriter->writeDump();
174	tim	1725
175	tim	1819	delete dumpWriter;
176			delete statWriter;
177	tim	1725
178	tim	1819	dumpWriter = NULL;
179			statWriter = NULL;
180
181	tim	1722	}
182
183	tim	1774	void VelocityVerletIntegrator::integrateStep() {
184	tim	1725
185	tim	1774	moveA();
186	tim	1819	calcForce(needPotential, needStress);
187	tim	1774	moveB();
188			}
189	tim	1725
190	tim	1774
191	tim	1819	void VelocityVerletIntegrator::calcForce(bool needPotential,
192			bool needStress) {
193	tim	1820	forceMan_->calcForces(needPotential, needStress);
194	tim	1722	}
195
196	tim	1820	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
197			return new DumpWriter(info_, info_->getDumpFileName());
198			}
199	tim	1722
200	tim	1820	StatWriter* VelocityVerletIntegrator::createStatWriter() {
201			return new StatWriter(info_->getStatFileName());
202			}
203
204
205	tim	1725	} //end namespace oopse